Plotting a Yeast RLS in Prism
'Plotting a Yeast RLS in Prism' Here is how to plot a completed yeast RLS experiment in Prism. 1. Log into CORE at http://data.kaeberleinlab.org/ . If you need a password for CORE, ask your mentor to email Brady and get you one. 2. In CORE, go to workflows > yeast RLS experiments. Select Kennedy Lab for "facility", and "completed" for status. Click SHOW. 3. Find your lifespan in the table by its description, and click the "view" link. 4. Download the last link under "reports", currently called "summary/NNN.xlsx", where NNN is the number of your RLS experiment. 5. Put your downloaded file alone in its own folder. I have a folder with all of my completed yeast RLS experiments, each in a numbered sub-folder labeled like: "NNN - description on lifespan expt" where NNN is the RLS experiment number. In the same folder, place your Perl script, in this case called from-rls-workflow-to-prism.pl, into the same folder as your data. NOTE: You will need to have Perl installed for this to work! (It is installed automagically on Mac or Linux, but not Windows). You should be able to get the correct version for your copy of Windows here http://www.activestate.com/activeperl/downloads . 6. Open the Excel spreadsheet in Excel or LibreOffice. open the second sheet / tab, "Lifespans". In Excel, save as "text (tab-delimited) (*.txt)". If using LibreOffice Calc, save as "text.csv", and select Field Delimiter to be {tab} and the Text Delimter to be NOTHING (make it blank). 7. Open a Terminal, AKA Command Prompt. In Windows, this is under start>all programs>accessories>command prompt. You might want to add a Command Prompt shortcut to your desktop. 8. The command prompt will open in your home directory C:\Users\YOURNAME\ . To move around, type CD "name of subdirectory" to go down, or cd .. to go up. To list everything in the directory you're in, type dir. To go down multiple directories at once, separate them with backslashes \ . For very long directory names, you can just begin to type them then press tab to have the rest filled in. 9. Navigate to the directory where your xlsx file and Perl script are. Type "perl from-rls-workflow-to-prism.pl" and press enter. (Hint: you can type perl fro and then press tab and enter). You should now see a new file in your folder. If your tab deleimted text file was called 919.txt, the new file will be 919output.xls. 10. This output file is your data in a Prism lifespan format. You can open an old prism file, delete the data from the DATA sheet, and copy-paste the entire sheet of your output file and save your new Prism file with a new name. To do this, select everything in the DATA sheet, ad right-click > delete, then paste in your data. 11. Go to Family in Prism (top left) and delete everything except the DATA sheet, usually called "Data 1". the click Results on the left, and select Survival Analyses>Survival Curve and press OK, Then change Tabulate: from precent survival to fraction survival, and select "None" under error bars in the next popup window, then click OK again. 12. Now you should have a graph. Begin formatting by using the Magic Wand, which is at the top under "Change"- and selecting another recently saved RLS plot. If you have never saved one before get a pzf file from someone else to get started! Edit the X-axis to say "Age (Generations)", and the Y-Axis to "Fraction Viable". Use size 2 for the data point symbols on the lines, and make sure that colors are consistent across related sets of plots, and that all gene names are correctly italicized, etc.